Data Quality and Calibration

def reset_dq_bits(input, bits, extver=None, extname='dq'):
    """
    Reset specified DQ values to 0 in FLT files.

    Parameters:
    - input: str or list, input FLT files to modify
    - bits: int or str, DQ bit values to reset (comma-separated string or integer)
    - extver: int, extension version to modify (default: all)
    - extname: str, extension name containing DQ array

    Returns:
    None (modifies input files in place)
    """

def run(configobj=None):
    """
    Processing function for resetbits task.

    Parameters:
    - configobj: ConfigObj, configuration with DQ bit parameters

    Returns:
    None (modifies input files)
    """

def main():
    """
    Command-line entry point for resetbits script.

    Returns:
    None
    """

def photeq(files='*_flt.fits', sciext='SCI', errext='ERR',
          readnoise=0.0, gain=1.0, platescale=1.0, exptime=1.0,
          expstart=0.0, **kwargs):
    """
    Equalize sensitivities across chips and epochs.

    Parameters:
    - files: str or list, input files for photometric equalization
    - sciext: str, science extension name
    - errext: str, error extension name
    - readnoise: float, detector read noise value
    - gain: float, detector gain value
    - platescale: float, pixel scale in arcsec/pixel
    - exptime: float, exposure time for normalization
    - expstart: float, exposure start time
    - **kwargs: dict, additional calibration parameters

    Returns:
    None (modifies input files with equalized values)
    """

def run(configObj):
    """
    Processing function for photeq task.

    Parameters:
    - configObj: ConfigObj, configuration with photometric parameters

    Returns:
    None (applies photometric equalization)
    """

def update(input, refdir="jref$", local=None, interactive=False,
          wcsupdate=True):
    """
    Update headers with ACS distortion reference files.

    Parameters:
    - input: str or list, input ACS files to update
    - refdir: str, directory containing reference files
    - local: str, local directory for reference files
    - interactive: bool, interactive mode for user prompts
    - wcsupdate: bool, update WCS after reference file update

    Returns:
    None (updates file headers)
    """

def run(configobj=None, editpars=False):
    """
    Processing function for updatenpol task.

    Parameters:
    - configobj: ConfigObj, configuration with update parameters
    - editpars: bool, allow parameter editing

    Returns:
    None (applies reference file updates)
    """

def main():
    """
    Command-line entry point for updatenpol script.

    Returns:
    None
    """

def replace(input, **pars):
    """
    Replace pixel values like NaNs with other values.

    Parameters:
    - input: str or list, input images to modify
    - **pars: dict, replacement parameters including:
        - mask_value: value to search for replacement
        - fill_value: replacement value
        - extensions: list of extensions to process

    Returns:
    None (modifies input images)
    """

def run(configobj):
    """
    Processing function for pixreplace task.

    Parameters:
    - configobj: ConfigObj, configuration with replacement parameters

    Returns:
    None (applies pixel value replacements)
    """

from drizzlepac import resetbits

# Reset cosmic ray and hot pixel flags
resetbits.reset_dq_bits('j8bt06nyq_flt.fits', bits='4096,8192')

# Reset specific bits for multiple files
input_files = ['file1_flt.fits', 'file2_flt.fits', 'file3_flt.fits']
resetbits.reset_dq_bits(input_files, bits='4096')  # Reset CR flag

# Command-line usage equivalent
# resetbits j8bt06nyq_flt.fits 4096,8192

from drizzlepac import photeq

# Basic photometric equalization
photeq.photeq(files='*_flt.fits',
             readnoise=3.1,
             gain=2.0,
             platescale=0.05)  # ACS/WFC pixel scale

# Multi-chip equalization with specific parameters
acs_files = ['j8bt06nyq_flt.fits', 'j8bt06nzq_flt.fits']
photeq.photeq(files=acs_files,
             sciext='SCI',
             errext='ERR',
             readnoise=3.1,
             gain=2.0)

from drizzlepac import updatenpol

# Update ACS files with latest distortion references
updatenpol.update('j8bt*_flt.fits',
                 refdir='jref$',
                 interactive=False,
                 wcsupdate=True)

# Update with local reference files
updatenpol.update('observation_flt.fits',
                 local='/path/to/local/refs/',
                 wcsupdate=True)

from drizzlepac import pixreplace

# Replace NaN values with zero
pixreplace.replace('image_with_nans.fits',
                  mask_value=float('nan'),
                  fill_value=0.0)

# Replace specific problematic values
pixreplace.replace('problematic_image.fits',
                  mask_value=-999.0,
                  fill_value=0.0,
                  extensions=['SCI', 'ERR'])

# Reset cosmic ray flags (bit 10, value 1024)
resetbits.reset_dq_bits(files, bits='1024')

# Reset multiple flags
resetbits.reset_dq_bits(files, bits='1024,4096')  # CR + saturation

# Reset all user-flagged bad pixels
resetbits.reset_dq_bits(files, bits='8192')

photeq_pars = {
    'readnoise': 3.1,    # e-/pixel
    'gain': 2.0,         # e-/DN
    'platescale': 0.05   # arcsec/pixel
}

photeq_pars = {
    'readnoise': 3.1,    # e-/pixel
    'gain': 1.5,         # e-/DN
    'platescale': 0.04   # arcsec/pixel
}

photeq_pars = {
    'readnoise': 2.5,    # e-/pixel
    'gain': 2.5,         # e-/DN
    'platescale': 0.13   # arcsec/pixel
}

# Verify successful DQ bit reset
from astropy.io import fits

with fits.open('processed_flt.fits') as hdul:
    dq_data = hdul['DQ', 1].data
    cr_pixels = (dq_data & 1024) > 0  # Check for remaining CR flags
    print(f"Remaining CR pixels: {cr_pixels.sum()}")